Analysis of the algorithm: From kernels to backup genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
biological_process 1 134 6.9968818026710595 11.431432499773674
cellular_component 1 40 4.162222345933308 5.25157343549579
disease 1 21 2.2250479846449136 2.909050012799259
genetic_interaction 1064.0 1070.0 1069.7655871845109 1069.7662188776321
molecular_function 1 26 3.028670320161523 3.71561924352452
pathway 1.0 191.0 4.003825833485152 8.704590940604282
phenotype 1 335 31.549734094937957 46.988832336933186
protein_interaction 1.0 729.0 29.8386134923593 54.03869234947398

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16997x16997 288898009 259379720
cellular_component_sim 17963x17963 322669369 322651406
disease_sim 4168x4168 17372224 16578192
genetic_interaction_sim 17354x17354 301161316 1862674
interaction_sim 16098x16098 259145604 479348
molecular_function_sim 17335x17335 300502225 300484890
paper_coDep_sim 3365x3365 11323225 132458
pathway_sim 3828x3828 14653584 159182
phenotype_sim 5077x5077 25775929 25770852
protein_interaction_sim 16098x16098 259145604 479348

Table 3. Filtered similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16994x16994 288796036 7665230
cellular_component_sim 4129x4129 17048641 282346
disease_sim 4008x4008 16064064 453776
molecular_function_sim 7683x7683 59028489 677260
pathway_sim 3423x3423 11716929 155500
phenotype_sim 4597x4597 21132409 534382

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process ct 16994x16994 288796036 288796036
biological_process el 16994x16994 288796036 288796036
biological_process ka 16994x16994 288796036 7682224
biological_process rf 16994x16994 288796036 288796036
cellular_component ct 4129x4129 17048641 17032131
cellular_component el 4129x4129 17048641 1598951
cellular_component ka 4129x4129 17048641 286475
cellular_component rf 4129x4129 17048641 1598951
disease ct 4008x4008 16064064 16064064
disease el 4008x4008 16064064 15968046
disease ka 4008x4008 16064064 457784
disease rf 4008x4008 16064064 15968046
genetic_interaction ct 17354x17354 301161316 297804049
genetic_interaction el 17354x17354 301161316 293368612
genetic_interaction ka 17354x17354 301161316 1880028
genetic_interaction rf 17354x17354 301161316 293368612
molecular_function ct 7683x7683 59028489 59020786
molecular_function el 7683x7683 59028489 27758757
molecular_function ka 7683x7683 59028489 684943
molecular_function rf 7683x7683 59028489 27758757
paper_coDep ct 3365x3365 11323225 11323225
paper_coDep el 3365x3365 11323225 9716415
paper_coDep ka 3365x3365 11323225 135823
paper_coDep rf 3365x3365 11323225 9716415
pathway ct 3423x3423 11716929 11710085
pathway el 3423x3423 11716929 8576601
pathway ka 3423x3423 11716929 158923
pathway rf 3423x3423 11716929 8576601
phenotype ct 4597x4597 21132409 21132409
phenotype el 4597x4597 21132409 19590157
phenotype ka 4597x4597 21132409 538979
phenotype rf 4597x4597 21132409 19590157
protein_interaction ct 16098x16098 259145604 259081193
protein_interaction el 16098x16098 259145604 252047984
protein_interaction ka 16098x16098 259145604 495446
protein_interaction rf 16098x16098 259145604 252047984

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
integration_mean_by_presence ct 19453x19453 378419209 342965046
integration_mean_by_presence el 19535x19535 381616225 363014718
integration_mean_by_presence ka 19535x19535 381616225 11243106
integration_mean_by_presence rf 19535x19535 381616225 362206934
mean ct 19453x19453 378419209 342965046
mean el 19535x19535 381616225 363014718
mean ka 19535x19535 381616225 11243106
mean rf 19535x19535 381616225 362206934

Weight values